title: What do you mean by transcription rate?: the conceptual difference between nascent transcription rate and mRNA synthesis rate is essential for the proper understanding of transcriptomic analyses.
abstract: mRNA synthesis in all organisms is performed by RNA polymerases, which work as nanomachines on DNA templates. The rate at which their product is made is an important parameter in gene expression. Transcription rate encompasses two related, yet different, concepts: the nascent transcription rate, which measures the in situ mRNA production by RNA polymerase, and the rate of synthesis of mature mRNA, which measures the contribution of transcription to the mRNA concentration. Both parameters are useful for molecular biologists, but they are not interchangeable and they are expressed in different units. It is important to distinguish when and where each one should be used. We propose that for functional genomics the use of nascent transcription rates should be restricted to the evaluation of the transcriptional process itself, whereas mature mRNA synthesis rates should be employed to address the transcriptional input to mRNA concentration balance leading to variation of gene expression.
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain.
authors.forename: José E
authors.initials: JE
authors.lastname: Pérez-Ortín
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Medina
authors.forename: Sebastián
authors.initials: S
authors.lastname: Chávez
authors.forename: Joaquín
authors.initials: J
authors.lastname: Moreno
mesh_terms: D012333:RNA, Messenger / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D015003:Yeasts / Q000235:genetics
chemical_list: D012333:RNA, Messenger
keywords: eukaryotes; mRNA synthesis; nascent transcription; transcription rate; yeast